14-52313933-C-G

Variant names:

• chr14-52313933-C-G
• rs2075797
• ENST00000691625.3:n.197G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691625.3(ENSG00000289424):​n.197G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,168 control chromosomes in the GnomAD database, including 2,422 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2422 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000691625.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 15 publications found

Genes affected

ENSG00000289424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289424	ENST00000691625.3	n.197G>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289424	ENST00000726798.1	n.134G>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289424	ENST00000726799.1	n.189G>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22934 AN: 152050 Hom.: 2423 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.162

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152168 Hom.: 2422 Cov.: 32 AF XY: 0.162 AC XY: 12027 AN XY: 74374

African (AFR) AF: 0.0965 AC: 4008 AN: 41540

American (AMR) AF: 0.264 AC: 4033 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2099 AN: 5138

South Asian (SAS) AF: 0.457 AC: 2199 AN: 4812

European-Finnish (FIN) AF: 0.120 AC: 1277 AN: 10598

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8337 AN: 67988

Other (OTH) AF: 0.165 AC: 348 AN: 2114

Alfa AF: 0.132 Hom.: 204

Bravo AF: 0.154

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		-0.67
PromoterAI		-0.0032	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2075797; hg19: chr14-52780651;